MultiQC Report

v1.20

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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.20

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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General Statistics

Showing ¹⁸/₁₈ rows and ³/₅ columns.

Sample Name	N50 (Kbp)	Assembly Length (Mbp)	M Reads	M Reads Mapped	% Reads Mapped
megahit_processed_B053323_contigs	101.4Kbp	4.4Mbp
megahit_processed_B053323_contigs.stat			1.1 M	1.1 M	99.8%
megahit_processed_B055059_contigs	53.8Kbp	4.5Mbp
megahit_processed_B055059_contigs.stat			1.7 M	1.7 M	99.9%
megahit_processed_B069073_contigs	67.8Kbp	4.3Mbp
megahit_processed_B069073_contigs.stat			1.4 M	1.4 M	99.2%
skesa_processed_B053323_contigs	61.5Kbp	4.4Mbp
skesa_processed_B053323_contigs.stat			1.1 M	1.1 M	99.4%
skesa_processed_B055059_contigs	41.1Kbp	4.4Mbp
skesa_processed_B055059_contigs.stat			1.7 M	1.7 M	99.3%
skesa_processed_B069073_contigs	46.2Kbp	4.2Mbp
skesa_processed_B069073_contigs.stat			1.4 M	1.4 M	98.4%
spades_processed_B053323_contigs	155.8Kbp	4.5Mbp
spades_processed_B053323_contigs.stat			1.1 M	1.1 M	99.9%
spades_processed_B055059_contigs	78.3Kbp	4.4Mbp
spades_processed_B055059_contigs.stat			1.7 M	1.7 M	99.9%
spades_processed_B069073_contigs	93.7Kbp	4.2Mbp
spades_processed_B069073_contigs.stat			1.4 M	1.4 M	99.3%

Sort	Group	Column	Description	ID	Scale
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly (kilo base pairs)	`N50`	None
\|\|	QUAST	Assembly Length (Mbp)	The total number of bases in the assembly (Mbp).	`Total length`	None
\|\|	Samtools	M Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	Samtools	% Reads Mapped	% Reads Mapped in the bam file	`mapped_passed_pct`	None

Sample Name	N50 (Kbp)	N75 (Kbp)	L50 (K)	L75 (K)	Largest contig (Kbp)	Length (Mbp)
megahit_processed_B053323_contigs	101.4Kbp	46.9Kbp	0.0K	0.0K	254.9Kbp	4.4Mbp
megahit_processed_B055059_contigs	53.8Kbp	30.8Kbp	0.0K	0.1K	135.6Kbp	4.5Mbp
megahit_processed_B069073_contigs	67.8Kbp	38.1Kbp	0.0K	0.0K	155.6Kbp	4.3Mbp
skesa_processed_B053323_contigs	61.5Kbp	37.1Kbp	0.0K	0.0K	193.5Kbp	4.4Mbp
skesa_processed_B055059_contigs	41.1Kbp	18.8Kbp	0.0K	0.1K	102.7Kbp	4.4Mbp
skesa_processed_B069073_contigs	46.2Kbp	22.9Kbp	0.0K	0.1K	137.6Kbp	4.2Mbp
spades_processed_B053323_contigs	155.8Kbp	86.7Kbp	0.0K	0.0K	379.4Kbp	4.5Mbp
spades_processed_B055059_contigs	78.3Kbp	47.0Kbp	0.0K	0.0K	178.0Kbp	4.4Mbp
spades_processed_B069073_contigs	93.7Kbp	58.0Kbp	0.0K	0.0K	185.1Kbp	4.2Mbp

Sample Name

megahit_processed_B053323_contigs

101.4Kbp

46.9Kbp

0.0K

254.9Kbp

4.4Mbp

megahit_processed_B055059_contigs

53.8Kbp

30.8Kbp

0.0K

0.1K

135.6Kbp

4.5Mbp

megahit_processed_B069073_contigs

67.8Kbp

38.1Kbp

0.0K

155.6Kbp

4.3Mbp

skesa_processed_B053323_contigs

61.5Kbp

37.1Kbp

0.0K

193.5Kbp

4.4Mbp

skesa_processed_B055059_contigs

41.1Kbp

18.8Kbp

0.0K

0.1K

102.7Kbp

4.4Mbp

skesa_processed_B069073_contigs

46.2Kbp

22.9Kbp

0.0K

0.1K

137.6Kbp

4.2Mbp

spades_processed_B053323_contigs

155.8Kbp

86.7Kbp

0.0K

379.4Kbp

4.5Mbp

spades_processed_B055059_contigs

78.3Kbp

47.0Kbp

0.0K

178.0Kbp

4.4Mbp

spades_processed_B069073_contigs

93.7Kbp

58.0Kbp

0.0K

185.1Kbp

4.2Mbp

Sample Name	Total Reads	Total Passed QC	Mapped	Supplementary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
megahit_processed_B053323_contigs.stat	1.1M	1.1M	1.1M	0.0M	0.0M	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M
megahit_processed_B055059_contigs.stat	1.7M	1.7M	1.7M	0.0M	0.0M	1.7M	1.6M	1.7M	0.0M	0.0M	0.0M
megahit_processed_B069073_contigs.stat	1.4M	1.4M	1.4M	0.0M	0.0M	1.4M	1.4M	1.4M	0.0M	0.0M	0.0M
skesa_processed_B053323_contigs.stat	1.1M	1.1M	1.1M	0.0M	0.0M	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M
skesa_processed_B055059_contigs.stat	1.7M	1.7M	1.7M	0.0M	0.0M	1.7M	1.6M	1.7M	0.0M	0.0M	0.0M
skesa_processed_B069073_contigs.stat	1.4M	1.4M	1.4M	0.0M	0.0M	1.4M	1.4M	1.4M	0.0M	0.0M	0.0M
spades_processed_B053323_contigs.stat	1.1M	1.1M	1.1M	0.0M	0.0M	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M
spades_processed_B055059_contigs.stat	1.7M	1.7M	1.7M	0.0M	0.0M	1.7M	1.7M	1.7M	0.0M	0.0M	0.0M
spades_processed_B069073_contigs.stat	1.4M	1.4M	1.4M	0.0M	0.0M	1.4M	1.4M	1.4M	0.0M	0.0M	0.0M

Sort	Column	Description	ID	Scale
\|\|	Total Reads	Total Reads	`flagstat_total`	read_count
\|\|	Total Passed QC	Total Passed QC	`total_passed`	read_count
\|\|	Mapped	Mapped	`mapped_passed`	read_count
\|\|	Supplementary Alignments	Supplementary Alignments	`supplementary_passed`	read_count
\|\|	Duplicates	Duplicates	`duplicates_passed`	read_count
\|\|	Paired in Sequencing	Paired in Sequencing	`paired in sequencing_passed`	read_count
\|\|	Properly Paired	Properly Paired	`properly paired_passed`	read_count
\|\|	Self and mate mapped	Reads with itself and mate mapped	`with itself and mate mapped_passed`	read_count
\|\|	Singletons	Singletons	`singletons_passed`	read_count
\|\|	Mate mapped to diff chr	Mate mapped to different chromosome	`with mate mapped to a different chr_passed`	read_count
\|\|	Diff chr (mapQ >= 5)	Mate mapped to different chromosome (mapQ >= 5)	`with mate mapped to a different chr (mapQ >= 5)_passed`	read_count

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